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P Bladon

Publications and source records attributed to P Bladon.

9 recordsLinked to original sources

Evaluation of a novel method for the identification of coevolving protein residues.

A novel method for the identification of correlated pairs in aligned homologous protein sequences is presented and evaluated against a model of simulated protein evolution incorporating covariation. Our method is shown to be capable of identifying all coevolutionary pairs of sites, with minimal interference by background correlations, in aligned sequence sets containing approximately 60 sequences with a tree depth of at least 30 accepted point mutations. This result is expected even in the presence of a large degree of neutral and non-correlated evolution. It is postulated that, since naturally occurring protein families may be subject to stronger selection pressures and a lesser degree of neutral evolution, this method of covariation analysis may be generally more robust than the model would indicate.

Amino Acid Sequence↗

Identification of a locality in snake venom alpha-neurotoxins with a significant compositional similarity to marine snail alpha-conotoxins: implications for evolution and structure/activity.

alpha-neurotoxins from elapid snake venoms and alpha-conotoxins from marine snails bind specifically and with high affinity to nicotinic cholinoceptors. Although both types of toxin are polypeptides, there is more than a fourfold difference in size between the two and no clear sequence homology is evident. A systematic computer search of the three-dimensional structure of erabutoxin b (an alpha-neurotoxin from the false sea snake Laticauda semifasciata) was performed to identify the locality that most closely matched the amino acid compositions of the smaller alpha-conotoxins (from the marine snails Conus magus and Conus geographus). The area of greatest similarity centered on residue position 25 of erabutoxin b, a locale that is conserved throughout the snake alpha-neurotoxins and their homologues. Six proteins unrelated to erabutoxin b were compared to the alpha-conotoxins to show that the extent of the erabutoxin b/alpha-conotoxin match was too high to be coincidental. Homologues of erabutoxin b, namely alpha-cobratoxin from Naja naja siamensis and cytotoxin VII4 from Naja mossambica mossambica, were also analyzed. The extent of the matching with the alpha-conotoxins decreased in the series erabutoxin b greater than alpha-cobratoxin greater than cytotoxin VII4, and this also relates the order of similarity to the pharmacological properties of the alpha-conotoxins. The alpha-conotoxin-like area of the snake alpha-neurotoxins is peripheral to the site previously considered important for binding to the cholinoceptor, even though it seems to represent the focus of evolutionary convergence between the two types of neurotoxin. The area of resemblance does, however, have strong associations with the conformational behavior of the snake toxins. Hence, the outcome of this study has important consequences for the current ideas on snake alpha-neurotoxin structure/activity relationships and the evolutionary origins of neurotoxicity.

Amino Acid Sequence↗

A method for detecting centres of natural selection in protein structures: potential for predicting the location of functional areas.

A simple method has been developed to detect protein microenvironments which are likely to be the focus of natural selection, and thereby important for function. It relies on distinguishing between the probability of an amino acid type arising by genetic mutation and the probability that it will be chosen by natural selection. When applied to proteins of known tertiary structure, the method revealed that major differences exist in the balance between neutral and selected change, and also that functional sites can be highlighted.

Animals↗

A simple method for aligning many protein sequences.

A simple extension of the Needleman and Wunsch algorithm for aligning pairs of protein sequences allows it to be used for the efficient generation of very large multiple-sequence alignments whose members are similar. This technique could have applications in a broad range of high-volume genomics projects.

Algorithms↗